Expansion of CAG/CTG repeats in DNA is the underlying cause of >14 genetic disorders, including Huntington disease (HD) and myotonic dystrophy. The mutational process is ongoing, with increases in repeat size enhancing the toxicity of the expansion in specific tissues. In many repeat diseases, the repeats exhibit high instability in the striatum, whereas instability is minimal in the cerebellum. In recent work using specific DNA repair assays, we have provided molecular insights into how the tissue-selective instability of CAG/CTG repeats may arise. In particular, our results show that the BER protein stoichiometry, overall nucleotide sequence, and DNA damage position can modulate repair outcome and that a suboptimal long-patch BER activity promotes CAG/CTG repeat instability. Moreover, we have found that the BER DNA glycosylase NEIL1 contributes to germline and somatic CAG repeat expansion in HD and that the binding and strand incision efficiency of the major human abasic endonuclease, APE1, is influenced by domain sequence, conformation, AP site location/relative positioning and duplex thermodynamic stability. Our results have both predictive and mechanistic implications for the success and failure of repair protein activity at such oxidatively sensitive, conformationally plastic/dynamic repetitive DNA domains. Single-strand break repair (SSBR) is an important subpathway of BER. Recent data has found a genetic linkage between proteins of SSBR aprataxin, tyrosyl-DNA phosphodiesterase 1 and DNA polynucleotide kinase phosphatase and human neurological disorders, implicating this repair mechanism in protection against neuronal cell loss and brain function. Ataxia with oculomotor apraxia 1 (AOA1) is caused by mutation in the APTX gene, which encodes the stand break repair protein aprataxin. Aprataxin removes 5-adenylate groups in DNA that arise from aborted ligation reactions. AOA1 is characterized by global cerebellar atrophy, highlighted by loss of Purkinje cells, ocular motor apraxia, and motor and sensory neuropathy. Strikingly, AOA1 patients lack the cancer susceptibility and other peripheral symptoms (e.g., immunological deficiencies) commonly associated with other inherited disorders stemming from a DNA repair defect. We have reported that aprataxin activity is necessary for maintaining optimal mitochondrial function, indicating that there is likely a mitochondrial component to the disease phenotype of AOA1. In a separate study, we have found that deficiency in a key SSBR/BER protein, i.e., XRCC1, is a risk factor for cellular damage caused by ischemic brain injury and impairs recovery following stroke induction. Additional studies have revealed that a modest decrement in SSBR/BER capacity, via polymerase haploinsufficiency, can render the brain more vulnerable to Alzheimer Disease (AD)-related molecular and cellular alterations. Lastly, our data indicate that because of their higher BER capacity, proliferative neural progenitor cells are more efficient at repairing DNA damage compared with their neuronally differentiated progeny, perhaps increasing the vulnerability of neurons to oxidative stress. Cockayne Syndrome (CS) is an autosomal recessive disorder, characterized by growth failure, neurological abnormalities, premature aging symptoms, and cutaneous photosensitivity, but no increased cancer incidence. CS is divided into two strict complementation groups: CSA (mutation in CKN1) and CSB (mutation in ERCC6). Of the patients suffering from CS, 80% have mutations in the CSB gene. Our past work has helped define the biochemical properties of CSB, revealing that the protein interacts with a diverse range of nucleic acid substrates and likely has important ATP-dependent and ATP-independent functions. Furthermore, results, obtained in collaboration with Dr. Vilhelm Bohr, suggest that CSB plays a role in both nuclear and mitochondrial BER, and may act as a mitochondrial DNA damage sensor, inducing mitochondrial autophagy in response to stress. While the CS proteins may participate in aspects of BER, in light of our recent observation that the CSB protein interacts with the 5 to 3 exonuclease, SNM1A, which has documented roles in the repair of DNA ICLs, my group favors the idea that deficiencies in the repair of endogenous transcription-blocking lesions underlie disease manifestation. Besides ICLs, such modifications could include bulky oxidative lesions, such as cyclopurines, as well as potentially DNA double-strand breaks (DSBs) as reported recently. In line with our hypothesis, we have found in laser microirradiation-confocal microscopy experiments that both CSA and CSB respond most robustly (in terms of kinetics and accumulation) to complex DNA damage, with ICLs > DSBs > bulky monoadducts > simple oxidative lesions. Notably, we were unable to see a convincing recruitment of CSA to sites of oxidative DNA damage, implying that simple BER lesions are not the primary substrates of the CS protein response. As such, a major focus of the project here is to define the molecular choreography of the emerging transcription-associated ICL repair response, and how it might engage both CSA and CSB. In addition, in light of unpublished observations, we are pursuing a two component hypothesis: (i) defects in the repair of transcription-blocking lesions contribute to the post-developmental tissue decline and mitochondrial dysfunction, and (ii) defects in nucleolar operations give rise to the profound developmental defects of the disease.